Functional significance of long non-coding RNAs in breast cancer

Breast Cancer

Volumn 21, Issue 5, 2014, Pages 515-521

  Vikram, Rajeev ^a   Ramachandran, Rahul ^b   Abdul, Khaja Shameem Mohammed ^c  

^a NOTTINGHAM TRENT UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^c UNIVERSITY OF RUHUNA   (Sri Lanka)

Author keywords

Breast cancer; lncRNA functions; Long non coding RNA; Regulatory RNA

Indexed keywords

LONG UNTRANSLATED RNA;

BREAST TUMOR; CLASSIFICATION; FEMALE; GENE EXPRESSION REGULATION; GENETICS; HUMAN; METABOLISM; PATHOLOGY;

BREAST NEOPLASMS; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; RNA, LONG NONCODING;

EID: 84931838508     PISSN: 13406868     EISSN: 18804233     Source Type: Journal    
DOI: 10.1007/s12282-014-0554-y     Document Type: Article

References (74)

1. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, et al. The transcriptional landscape of the mammalian genome. Science. 2005;309:1559–63.
2. Kapranov P. Studying chromosome-wide transcriptional networks: new insights into disease? Genome Med. 2009;1:50.
3. Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into functions. Nat Rev Genet. 2009;10:155–9.
4. Van Bakel H, Hughes TR. Establishing legitimacy and function in the new transcriptome. Brief Funct Genomic Proteomic. 2009;8:424–36.
5. Wang J, Zhang J, Zheng H, Li J, Liu D, Li H, et al. Mouse transcriptome: neutral evolution of “non-coding” complementary DNAs. Nature. 2004;431:1.
6. Struhl K. Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nat Struct Mol Biol. 2007;14:103–5.
7. Van Bakel H, Nislow C, Blencowe BJ, Hughes TR. Most “dark matter” transcripts are associated with known genes. PLoS Biol. 2010;8:e1000371.
8. Wilusz JE, Sunwoo H, Spector DL. Long noncoding RNAs: functional surprises from the RNA world. Genes Dev. 2009;23:1494–504.
9. Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell. 2009;136:629–41.
10. Mitra S, Mitra AP, Triche TJ. A central role for long non-coding RNA in cancer. Front Genet. 2012;3:17.
11. Hung T, Chang HY. Long noncoding RNA in genome regulation: prospects and mechanisms. RNA Biol. 2010;7:582–5.
12. Moazed D. Small RNAs in transcriptional gene silencing and genome defence. Nature. 2009;457:413–20.
13. Carthew RW, Sontheimer EJ. Origins and mechanisms of miRNAs and siRNAs. Cell. 2009;136:642–55.
14. Siomi H, Siomi MC. On the road to reading the RNA-interference code. Nature. 2009;457:396–404.
15. Brennecke J, Aravin AA, Stark A, Dus M, Kellis M, Sachidanandam R, et al. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell. 2007;128:1089–103.
16. Wang KC, Chang HY. Molecular mechanisms of long noncoding RNAs. Mol Cell. 2011;43:904–14.
17. Nagano T, Fraser P. No-nonsense functions for long noncoding RNAs. Cell. 2011;145:178–81.
18. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science. 2007;316:1484–8.
19. Wu JM, Fackler MJ, Halushka MK, Molavi DW, Taylor ME, Teo WW, et al. Heterogeneity of breast cancer metastases: comparison of therapeutic target expression and promoter methylation between primary tumors and their multifocal metastases. Clin Cancer Res. 2008;14:1938–46.
20. Khalil AM, Rinn JL. RNA–protein interactions in human health and disease. Semin Cell Dev Biol. 2011;22:359–65.
21. Wang X, Song X, Glass CK, Rosenfeld MG. The long arm of long noncoding RNAs: roles as sensors regulating gene transcriptional programs. Cold Spring Harb Perspect Biol. 2011;3:a003756.
22. Wapinski O, Chang HY. Long noncoding RNAs and human disease. Trends Cell Biol. 2011;21:354–61.
23. Kosir M, Jia H, Ju D, Lipovich L. Challenging paradigms: long non-coding RNAs in breast ductal carcinoma in situ (DCIS). Front Genet. 2013;4:50.
24. Sun M, Kraus WL. Minireview: long noncoding RNAs: new “links” between gene expression and cellular outcomes in endocrinology. Mol Endocrinol. 2013;27:1390–402.
25. Nagano K. Search for breast cancer-related biomarker proteins for drug discovery (in Japanese with English abstract). Yakugaku Zassh. 2010;130:1701–6.
26. Negrini M, Nicoloso MS, Calin GA. MicroRNAs and cancer—new paradigms in molecular oncology. Curr Opin Cell Biol. 2009;21:470–9.
27. Bánfai B, Jia H, Khatun J, Wood E, Risk B, Gundling WE, et al. Long noncoding RNAs are rarely translated in two human cell lines. Genome Res. 2012;22:1646–57.
28. Sleutels F, Zwart R, Barlow DP. The non-coding air RNA is required for silencing autosomal imprinted genes. Nature. 2002;415:810–3.
29. Seidl CIM, Stricker SH, Barlow DP. The imprinted Air ncRNA is an atypical RNAPII transcript that evades splicing and escapes nuclear export. EMBO J. 2006;25:3565–75.
30. Nagano T, Fraser P. Emerging similarities in epigenetic gene silencing by long noncoding RNAs. Mamm Genome. 2009;20:557–62.
31. Willingham AT, Orth AP, Batalov S, Peters EC, Wen BG, Aza-Blanc P, et al. A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science. 2005;309:1570–3.
32. Fejes-Toth K, Sotirova V, Sachidanandam R, Assaf G, Hannon GJ, Kapranov P, et al. Post-transcriptional processing generates a diversity of 5’-modified long and short RNAs. Nature. 2009;457:1028–32.
33. Tam OH, Aravin AA, Stein P, Girard A, Murchison EP, Cheloufi S, et al. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature. 2008;453:534–8.
34. Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi-Miyagawa S, Obata Y, et al. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature. 2008;453:539–43.
35. Czech B, Malone CD, Zhou R, Stark A, Schlingeheyde C, Dus M, et al. An endogenous small interfering RNA pathway in Drosophila. Nature. 2008;453:798–802.
36. Okamura K, Chung W-J, Ruby JG, Guo H, Bartel DP, Lai EC. The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs. Nature. 2008;453:803–6.
37. Munroe SH, Lazar MA. Inhibition of c-erbA mRNA splicing by a naturally occurring antisense RNA. J Biol Chem. 1991;266:22083–6.
38. Beltran M, Puig I, Peña C, García JM, Alvarez AB, Peña R, et al. A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes Dev. 2008;22:756–69.
39. Cai X, Cullen BR. The imprinted H19 noncoding RNA is a primary microRNA precursor. RNA. 2007;13:313–6.
40. Cunnington MS, Koref MS, Mayosi BM, Burn J, Keavney B. Chromosome 9p21 SNPs associated with multiple disease phenotypes correlate with ANRIL expression. PLoS Genet. 2010;6:e1000899.
41. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature. 2010;464:1071–6.
42. Lai M, Yang Z, Zhou L, Zhu Q, Xie H, Zhang F, et al. Long non-coding RNA MALAT-1 overexpression predicts tumor recurrence of hepatocellular carcinoma after liver transplantation. Med Oncol. 2012;29:1810–6.
43. Loi S, Haibe-Kains B, Desmedt C, Lallemand F, Tutt AM, Gillet C, et al. Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade. J Clin Oncol. 2007;25:1239–46.
44. Iacoangeli A, Lin Y, Morley EJ, Muslimov IA, Bianchi R, Reilly J, et al. BC200 RNA in invasive and preinvasive breast cancer. Carcinogenesis. 2004;25:2125–33.
45. Lottin S. Overexpression of an ectopic H19 gene enhances the tumorigenic properties of breast cancer cells. Carcinogenesis. 2002;23:1885–95.
46. Berteaux N, Lottin S, Monté D, Pinte S, Quatannens B, Coll J, et al. H19 mRNA-like noncoding RNA promotes breast cancer cell proliferation through positive control by E2F1. J Biol Chem. 2005;280:29625–36.
47. Huang J, Zhou N, Watabe K, Lu Z, Wu F, Xu M, et al. Long non-coding RNA UCA1 promotes breast tumor growth by suppression of p27 (Kip1). Cell Death Dis. 2014;5:e1008.
48. Stratton MR, Campbell PJ, Futreal PA. The cancer genome. Nature. 2009;458:719–24.
49. Cayre A, Rossignol F, Clottes E, Penault-Llorca F. aHIF but not HIF-1alpha transcript is a poor prognostic marker in human breast cancer. Breast Cancer Res. 2003;5:R223–30.
50. Rossignol F, Vaché C, Clottes E. Natural antisense transcripts of hypoxia-inducible factor 1alpha are detected in different normal and tumour human tissues. Gene. 2002;299:135–40.
51. Chen W, Böcker W, Brosius J, Tiedge H. Expression of neural BC200 RNA in human tumours. J Pathol. 1997;183:345–51.
52. Mourtada-Maarabouni M, Pickard MR, Hedge VL, Farzaneh F, Williams GT. GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer. Oncogene. 2009;28:195–208.
53. Mourtada-Maarabouni M, Hedge VL, Kirkham L, Farzaneh F, Williams GT. Growth arrest in human T-cells is controlled by the non-coding RNA growth-arrest-specific transcript 5 (GAS5). J Cell Sci. 2008;121:939–46.
54. Giannoukakis N, Deal C, Paquette J, Goodyer CG, Polychronakos C. Parental genomic imprinting of the human IGF2 gene. Nat Genet. 1993;4:98–101.
55. Ariel I. The imprinted H19 gene is a marker of early recurrence in human bladder carcinoma. Mol Pathol. 2000;53:320–3.
56. Lustig-Yariv O, Schulze E, Komitowski D, Erdmann V, Schneider T, de Groot N, et al. The expression of the imprinted genes H19 and IGF-2 in choriocarcinoma cell lines. Is H19 a tumor suppressor gene? Oncogene. 1997;15:169–77.
57. Adriaenssens E, Dumont L, Lottin S, Bolle D, Leprêtre A, Delobelle A, et al. H19 overexpression in breast adenocarcinoma stromal cells is associated with tumor values and steroid receptor status but independent of p53 and Ki-67 expression. Am J Pathol. 1998;153:1597–607.
58. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell. 2007;129:1311–23.
59. Silva JM, Boczek NJ, Berres MW, Ma X, Smith DI. LSINCT5 is over expressed in breast and ovarian cancer and affects cellular proliferation. RNA Biol. 2011;8:496–505.
60. Bernard D, Prasanth KV, Tripathi V, Colasse S, Nakamura T, Xuan Z, et al. A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO J. 2010;29:3082–93.
61. Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, Watt AT, et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell. 2010;39:925–38.
62. Tripathi V, Shen Z, Chakraborty A, Giri S, Freier SM, Wu X, et al. Long noncoding RNA MALAT1 controls cell cycle progression by regulating the expression of oncogenic transcription factor B-MYB. PLoS Genet. 2013;9:e1003368.
63. Geirsson A, Lynch RJ, Paliwal I, Bothwell ALM, Hammond GL. Human trophoblast noncoding RNA suppresses CIITA promoter III activity in murine B-lymphocytes. Biochem Biophys Res Commun. 2003;301:718–24.
64. Geirsson A, Bothwell ALM, Hammond GL. Inhibition of alloresponse by a human trophoblast non-coding RNA suppressing class II transactivator promoter III and major histocompatibility class II expression in murine B-lymphocytes. J Heart Lung Transplant. 2004;23:1077–81.
65. Lanz RB, McKenna NJ, Onate SA, Albrecht U, Wong J, Tsai SY, et al. A steroid receptor coactivator, SRA, functions as an RNA and is present in an SRC-1 complex. Cell. 1999;97:17–27.
66. Lanz RB, Chua SS, Barron N, Soder BM, DeMayo F, O’Malley BW. Steroid receptor RNA activator stimulates proliferation as well as apoptosis in vivo. Mol Cell Biol. 2003;23:7163–76.
67. Leygue E, Dotzlaw H, Watson PH, Murphy LC. Expression of the steroid receptor rna activator in human breast tumors. Cancer Res. 1999;59:4190–3.
68. Murphy LC, Simon SLR, Parkes A, Leygue E, Dotzlaw H, Snell L, et al. altered expression of estrogen receptor coregulators during human breast tumorigenesis. Cancer Res. 2000;60:6266–71.
69. Wang F, Li X, Xie X, Zhao L, Chen W. UCA1, a non-protein-coding RNA up-regulated in bladder carcinoma and embryo, influencing cell growth and promoting invasion. FEBS Lett. 2008;582:1919–27.
70. Erwin JA, Lee JT. New twists in X-chromosome inactivation. Curr Opin Cell Biol. 2008;20:349–55.
71. Benoît M-H, Hudson TJ, Maire G, Squire JA, Arcand SL, Provencher D, et al. Global analysis of chromosome X gene expression in primary cultures of normal ovarian surface epithelial cells and epithelial ovarian cancer cell lines. Int J Oncol. 2007;30:5–17.
72. Yildirim E, Kirby JE, Brown DE, Mercier FE, Sadreyev RI, Scadden DT, et al. Xist RNA is a potent suppressor of hematologic cancer in mice. Cell. 2013;152:727–42.
73. Askarian-Amiri ME, Crawford J, French JD, Smart CE, Smith MA, Clark MB, et al. SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer. RNA. 2011;17:878–91.
74. Raouf A, Sun Y, Chatterjee S, Basak P. The biology of human breast epithelial progenitors. Semin Cell Dev Biol. 2012;23:606–12.